TB-Profiler result

Run: ERR7801194
Summary

Run ID: ERR7801194

Sample name:

Date: 02-04-2023 05:58:33

Number of reads: 659641

Percentage reads mapped: 99.11

Strain: lineage4.3.3

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
pncA 2288727 p.Leu172Pro missense_variant 1.0 pyrazinamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490904 p.Phe41Ser missense_variant 0.1
mshA 575833 c.486C>T synonymous_variant 0.13
mshA 575917 c.570C>T synonymous_variant 0.14
mshA 575969 p.Asp208Tyr missense_variant 0.22
mshA 576316 c.969A>G synonymous_variant 1.0
ccsA 620427 c.537C>A synonymous_variant 0.15
rpoB 759623 c.-184C>A upstream_gene_variant 0.13
rpoB 761171 c.1365C>T synonymous_variant 0.12
rpoB 761572 p.Pro589His missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766709 p.Gly1114Cys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779480 p.Asp164Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416706 c.642C>T synonymous_variant 0.96
atpE 1460862 c.-183T>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474672 n.1015C>A non_coding_transcript_exon_variant 0.12
rrl 1475009 n.1352G>T non_coding_transcript_exon_variant 0.15
tlyA 1917783 c.-157G>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102638 c.405A>T synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.28
PPE35 2170053 p.Thr187Ser missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2747399 p.Ile67Thr missense_variant 0.2
folC 2747646 c.-48G>T upstream_gene_variant 0.17
ribD 2987138 c.300C>A synonymous_variant 0.18
Rv2752c 3064676 p.Pro506Ser missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339213 c.96G>A synonymous_variant 0.15
Rv3083 3448617 c.114G>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612141 p.Ala326Ser missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039919 c.786C>T synonymous_variant 0.2
clpC1 4040223 p.Glu161Gly missense_variant 0.17
embC 4240448 p.Gln196Lys missense_variant 0.12
embA 4242322 c.-911C>T upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243542 p.Gly104Trp missense_variant 0.17
embA 4243879 p.Val216Glu missense_variant 0.13
embA 4244854 p.Val541Ala missense_variant 0.2
embA 4244858 c.1626G>T synonymous_variant 0.22
embA 4244861 c.1629G>C synonymous_variant 0.22
embA 4244863 p.Leu544Gln missense_variant 0.22
embA 4244865 p.Ala545Pro missense_variant 0.22
embA 4244871 p.Gly547His missense_variant 0.22
embB 4247102 p.Pro197Thr missense_variant 0.13
embB 4249079 p.Ser856Arg missense_variant 1.0
embB 4249366 p.Glu951Asp missense_variant 0.14
aftB 4267933 p.Ala302Ser missense_variant 0.22
ubiA 4269918 c.-85G>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0